MediaMonkey uses the Android audio engine, and plays any formats that are supported by a device's implementation of the engine (see: http://developer.android.com/guide/appendix/media-formats.html ). If your Android device exhibits stuttering/clicks/faulty playback it's most likely due to an issue with your device's support for a particular audio format. You can verify this by playing the same file in the Google Play music.

To work around such issues you can: - delete all problematic files from the device - in MediaMonkey for Windows, in Tools > Options > Portable devices, set flac (or whatever format results in playback problems) as an unsupported format in your device's auto-conversion settings. That way, when syncing, flac tracks will be auto-converted to a format that is supported on the device.